More than half (53 per cent) of eligible members took part in the ballot, with only 2 per cent voting to accept the pay rise that has been offered.
EIS general secretary Larry Flanagan said the result of the vote showed teachers considered the pay offer to be “neither fair nor acceptable”.
Teachers in the NASUWT had already rejected the proposed pay deal earlier in January.
And EIS leaders said they now expected an “enhanced offer” would be made when the unions meet with the Scottish Government and the local government body, Cosla, next week.
But the union warned it would also be considering the “next steps” as it insisted politicians “cannot take the goodwill of teachers for granted”.
Mr Flanagan said: “Scotland’s teachers deserve a fair pay rise from their employers and the Scottish Government.
“With this ballot result, our members have shown, very clearly, that they consider the current offer neither fair nor acceptable.
“Throughout the continuing Covid crisis, Scotland’s teachers have worked flat out to seek to minimise the damaging impact of the pandemic on young people’s education.
“Teachers are key to the planned programme of educational recovery and deserve to be appropriately remunerated for their efforts.
“It is time for Cosla and the Scottish Government to play fair and finally commit to a reasonable and fair pay rise for Scotland’s teaching professionals.”
The salary increase being negotiated is for the year 2021/22, with the EIS saying it would see all grades of teaching staff being given a 1 per cent rise effective from April 2021, with a further 1 per cent as of January 2022.
There would also be a one-off payment of £100 for each staff member on the date the offer is agreed – though part-time teachers would receive less.
And for those earning more than £80,000 per annum, the salary rise would be capped at £800.
EIS salaries convener Des Morris said: “Scotland’s teachers have sent a very strong and very clear message with this ballot result.”